Identification of Rodents

SUBJECT:

Identification of Rodents

 Effective Date:
9/26/2025 		Policy Number:
10.4.8
听 Supersedes:
9/30/2022
9/27/2019
8/30/2016 		Page 1 of 5
听 Responsible Authorities:
Principal Investigator
Vice President, Research
Institutional Animal Care and Use Committee
Associate Vice President for Research, Research Integrity
Comparative Medicine
  1. Background

    The Public Health Service (PHS) policy and the Guide for the Care and Use of Laboratory Animals (the Guide) require the Institutional Animal Care and Use Committee (IACUC) and the Attending Veterinarian to provide oversight of all experimental procedures and guarantee the welfare of the animals used in biomedical research. As stated in the NIH Guidelines for the Genotyping of Mice and Rats, specific genetic identification of pups in a litter is critical to the efficient pursuit of research and reducing the number of animals used.

  2. Purpose

    The purpose of this document is to provide guidelines to researchers and animal care staff regarding acceptable methods of individual identification of mice and rats.

  3. General Statement

    Properly executed procedures will protect the welfare of animals used and avoid exposing the animals to undue stress and pain. Periodic genetic monitoring of genetically engineered animals is recommended to ensure that the expected strains are being propagated and to mitigate the effects of genetic drift.

  4. Definitions
    1. Genetically modified animal (GMA) is an animal whose genetic material has been altered by adding, changing, or removing certain DNA sequences in a way that does not occur under natural conditions.
    2. A mouse or rat strain is a group of animals that is genetically uniform, which can be inbred, mutated, or genetically engineered/modified. Inbred strains can genetically diverge into substrains under various circumstances (e.g., a breeding colony of an inbred strain maintained at different locations).
    3. Genotyping is the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence.
    4. Nomenclature as related to this policy is an international system of standardized genetic terms and symbols applied to rodent strains/substrains.
  5. Policy
    1. Cage cards are used for the identification of animals within a cage. However, it is often advantageous or necessary to identify experimental animals individually (see page 5 for chart of pros/cons of each system).
    2. Temporary marking systems acceptable for rodents include fur clipping and shaving in distinct configurations on the animal's body, non-toxic waterproof dyes, and nontoxic colored markers applied in a variety of patterns on light-colored fur or hairless areas on the tail.
    3. Permanent identification systems (See CM SOP #410 "Rodent Identification and Genotyping" for detailed procedures)
      1. Ear pinna biopsy (commonly referred to as 'ear punch' or 'ear notch'): Uses removal of ear tissue in a standardized series of circles and/or notches to represent a number
      2. Ear tags: attachment of a tag with a unique identification number
      3. Microchip transponder
      4. Tattoos
      5. Distal phalanx biopsy (commonly referred to as 'toe clipping')
        1. May be approved by the IACUC only after all other alternatives have been considered and a sound justification provided, especially if it serves a dual purpose of identification and tissue collection for genotyping.
        2. Must only be used in altricial, pre-weanling mice or rats up to 7 days of age.
        3. Only the most distal bone of the toe (3rd phalanx) and only one toe per paw may be removed.
    4. Research faculty and staff performing tissue collection procedures for genotyping and permanent identification methods must be trained and proficient in the procedures.
    5. Investigators who use rodent models are responsible for accurate reporting of the identification of research rodents with regard to strain/substrain and genetic background. To that end, researchers are strongly encouraged to follow standardized nomenclature guidelines (available at MGI-Mouse Nomenclature ).
  6. Accountability

    The Principal Investigator (PI) will be responsible for:

    • Describing all procedures performed on an animal including the tissue collection for genotyping and individual identification method in sufficient detail in any IACUC protocol.
    • Ensuring appropriate training of personnel performing the genotyping or identification procedures and contact the Comparative Medicine staff for support or any concern/problem resolution.
    • Securing the usage of proper nomenclature of mouse and rat strains/substrains during the conduct of the research study and in publications.
    • Ensuring the use of anesthetics and analgesics as required in this Policy.

    The IACUC will be responsible for:

    • Reviewing and approving, requiring modifications in (to secure approval) or withholding approval of IACUC protocols and/or amendments, especially assessing the appropriateness of the procedures described for genotyping and identification of animals.
    • Reviewing records on a regular basis during semi-annual site inspections, post-approval monitoring reviews, and whenever concerns regarding the welfare of a particular animal(s) arise.

    The Research Integrity office will be responsible for:

    • Administrative support of the IACUC members to facilitate their regulatory function.
    • Maintaining policy and assure regular review and update as necessary by the IACUC.
    • Organizing, supporting and recording outcomes of regular inspections of research labs in regards to procedures performed and nomenclature used.

    The Attending Veterinarian/Office of Comparative Medicine (CM) will be responsible for:

    • Ensuring adequate oversight of experimental procedures including consultation during the design of the study, evaluation of recordkeeping, health surveillance of the animal colonies, and the assessment of the well-being of animals on a one-by-one basis.
    • Provide training to research and animal care personnel performing collection of tissues for genotyping and identification procedures.
  7. Policy Renewal Date

    9/26/2028

References

  1. Guide for the Care and Use of Laboratory Animals, 8th ed
  2. Castelhano-Carlos MJ, Sousa N, Ohl F, Baumans V. Identification methods in newborn C57BL/6 mice: a developmental and behavioural evaluation. Lab Anim 44, 1-16. 2010
  3. Hankenson FC, Garzel LM, Fischer DD, Nolan B, Hankenson KD. Evaluation of tail biopsy collection in laboratory mice (Mus musculus): vertebral ossification, DNA quantity, and acute behavioral responses. J Am Assoc Lab Anim Sci. 47(6): 10-18. 2008
  4. Meldgaard M, Bollen PJA, Finsen B. Non-invasive method for sampling and extraction of mouse DNA for PCR. Laboratory Animals 38, 413-417. 2004
  5. Montoliu L, Whitelaw CB. Using standard nomenclature to adequately name transgenes, knockout gene alleles and any mutation associated to a genetically modified mouse strain. Transgenic Res 20 (2): 435-440. 2010
  6. NIH Guidelines for the Genotyping of Rodents.
  7. Paluch LR, Lieggii CC, Dumont M, Monette S, Riedel E, Lipman NS. Developmental and Behavioral Effects of Toe Clipping on Neonatal and Preweanling Mice with and without Vapocoolant Anesthesia. JAALAS 53(2): 132-140. 2014
  8. Penn State IACUC Guidelines.

POLICY APPROVAL

Initiating Authority

Gregg B. Fields, Ph.D., Vice President for Research
10-13-25

Executed signature pages are available in the Initiating Authority Office

Method Genotyping Identification Use Pros Cons
Ear Punch / Notch Yes Yes (permanent notch pattern)
  • Dual purpose (sample + ID)
  • Inexpensive
  • Quick, no anesthesia
  • Permanent ID if done after weaning
  • Limited number of unique codes
  • If done too early, holes can close
  • Requires training for accuracy
Tail Snip Yes No (not used for ID)
  • Relatively large tissue sample
  • Commonly used, easy to genotype
  • May require anesthesia/analgesia
  • Not an ID method
  • Increased welfare concerns
Microchip (RFID) No Yes (unique electronic ID)
  • Permanent and unique ID
  • Easy electronic tracking
  • Suitable for large colonies
  • Higher cost per animal
  • Requires special scanner
  • Minor procedure with injection
Tattoo (digit, tail, ear) No Yes (permanent ink ID)
  • Permanent, inexpensive
  • Works for neonates
  • Large number of possible IDs
  • Not a tissue source
  • Fading/blurring possible
  • Requires training and equipment
Ear Tag No Yes (metal/plastic tag)
  • Inexpensive
  • Easy to apply
  • Tags can fall out
  • Can cause tearing/infection
  • Not a tissue source
Fur Marking (dye, Sharpie) No Yes (temporary)
  • Non-invasive
  • Very low cost
  • Good for short-term ID
  • Temporary only (not permanent)
  • Not a tissue source
  • Fades with grooming/shed
Distal Phalanx Biopsy ('toe clip') Yes Yes
  • Permanent ID
  • Can be used for genotyping
  • Reliable for small litters or very young neonates (<PND 7)
  • Invasive
  • Not scalable to large colonies
  • Not visually readable at a distance
  • Welfare concerns (may require anesthesia/analgesia)